title: Genome-wide transcriptome profiling of Colon Intestine-Chip and Conventional Organoid Cell Culture System Using RNA-seq

city: Boston

first: Lorna

last: Ewart

state: MA

address: 27 Drydock Avenue

institute: Emulate Inc.

summary: goal of this study was A) to compare global RNA-sequencing (RNA-seq) profiles data of organoid- derived colonic epithelial cells cultured and differentiated in i) conventional suspension organoids cultures (n=3), ii) Colon Intestine-Chips cultured for 5 days under constant flow, without endothelium and stretch (n=4), iii) Colon Intestine-Chips cultured for 5 days under constant flow, without endothelium and with stretch (n=4), iv) Colon Intestine-Chips cultured for 5 days under constant flow, with endothelium and without stretch (n=4), v) Colon Intestine-Chips cultured for 5 days under constant flow, with endothelium and stretch (n=6), vi) Colon Intestine-Chips cultured for 8 days under constant flow, without endothelium and stretch (n=4), vii) Colon Intestine-Chips cultured for 8 days under constant flow, without endothelium and with stretch (n=4), viii) Colon Intestine-Chips cultured for 8 days under constant flow, with endothelium and without stretch (n=4), ix) Colon Intestine-Chips cultured for 8 days under constant flow, with endothelium and stretch (n=3), and B) to identify differences in transcriptome profiles of organoid- derived colonic epithelial cells between following two conditions, unstimulated and basolaterally stimulated with IL-22 (10pM, 100pM or 1nM) Colon Intestine-Chips.

overall_design:
Global RNA expression profiles of Colon Intestine-Chip Day 5 cultured without endothelium and stretch (n=4 epithelial channel); Colon Intestine-Chip Day 5 cultured without endothelium and with stretch (n=4 epithelial channel); Colon Intestine-Chip Day 5 cultured with endothelium and without stretch (n=4 epithelial channel); Colon Intestine-Chip Day 5 cultured with endothelium and stretch (n= 6 epithelial channel); Colon Intestine-Chip Day 8 cultured without endothelium and stretch (n=4 epithelial channel); Colon Intestine-Chip Day 8 cultured without endothelium and with stretch (n=4 epithelial channel); Colon Intestine-Chip Day 8 cultured with endothelium and without stretch (n=4 epithelial channel); Colon Intestine-Chip Day 8 cultured with endothelium and stretch (n= 3 epithelial channel)Conventional suspension organoid culture systems Day 0 (n=3 upper compartment); untreated Colon Intestine-Chips (n=3 epithelial channel); treated Colon Intestine-Chips with 10pM IL-22 (n=3 epithelial channel); treated Colon Intestine-Chips with 100pM IL-22 (n=3 epithelial channel); treated Colon Intestine-Chips with 1nM IL-22 (n=3 epithelial channel) were generated by deep sequencing using Illumina HiSeq.
Colonic epithelial cells (CoEpiCs).

first: Athanasia

last: Apostolou

first: Dimitris

last: Manatakis

first: Maria

last: Paraskevopoulou

first: Rohit

last: Pachakshari


title: Human ESC differentiation into cranial neural crest cells in the presence of PhenDC3

status: Public on Nov 10 2021

city: Manchester

first: Angela

last: Simeone

address: 200 Hathersage Rd

country: United Kingdom

institute: Genomic Services QIAGEN

type: Expression profiling by high throughput sequencing

summary: Human ESC differentiation into cranial neural crest cells in the presence of PhenDC4. Human embryonic stem cells (hESC) were differentiated into cranial neural crest cells in presence of the G-quadruplex stabilising ligand PhenDC3 or DMSO control. The case when no PhenDC3 or DMSO have been included in the differentiation protocol represent an additional control experiment.

first: Katherine

middle: G

last: Zyner

first: David

last: Tannahill

first: Shankar

last: Balasubramanian


title: High expression profiling analysis of the early response to spinal cord injury identified a key role for mTORC1 signaling

city: Santiago

first: Juan

last: Larraín

address: Portugal 49

department: Cellular and Molecular Biology

country: Chile

institute: Pontificia Universidad Catolica de Chile

summary: Xenopus laevis are able to regenerate the spinal cord during larvae stages through the activation of neural stem progenitor cells (NSPC). Here, we use high-resolution expression profiling to characterize the early transcriptome changes induced after spinal cord injury, and identify the signals that trigger NSPC proliferation. The analysis delineates a pathway that starts with a rapid and transitory activation of immediate early genes, followed by migration processes and immune response genes, the pervasive increase of NSPC specific ribosome biogenesis factors, and genes involved in stem cell proliferation. Western blot and immunofluorescence analysis showed that mTORC1 is rapidly and transiently activated after SCI, and its pharmacological inhibition impairs spinal cord regeneration, and proliferation of NSPC of genes involved in the G1/S transition of cell cycle, with a strong effect on PCNA. We propose that the mTOR signaling pathway is a key player in the activation of NPSCs during the early steps of spinal cord regeneration.

overall_design: Time-series analysis of the early transcriptional changes deployed in response to spinal cord injury in regenerative stage of Xenopus laevis.

first: Johany

last: Peñailillo

first: Miriam

last: Palacios

first: Constanza

last: Mounieres

first: Elena

last: De Domenico

first: Ilya

last: Patrushev

first: Mike

last: Gilchrist


title: Integrator enforces the fidelity of transcriptional termination at protein-coding genes

city: Miami

first: Felipe

last: Beckedorff

state: FL

address: 1501 NW 10th Avenue room 731.G , Miami, FL

country: USA

institute: University of Miami

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Integrator regulates the 3’-end processing and termination of multiple classes of noncoding RNAs. Depletion of INTS11, the catalytic subunit of Integrator, or ectopic expression of its catalytic dead enzyme impairs the 3’-end processing and termination of a set of protein coding transcripts termed Integrator-regulated termination (IRT) genes. This defect is manifested by increased RNA polymerase II (RNAPII) readthrough and occupancy of serine-2 phosphorylated RNAPII, de-novo trimethylation of lysine 36 on histone H3, and a compensatory elevation of the cleavage and polyadenylation (CPA) complex in the downstream regions. 3’-RNA-sequnecing reveals that proximal polyadenylation site usage relies on the endonuclease activity of INTS11. The DNA sequence encompassing the transcription end sites of IRT genes feature downstream polyadenylation motifs and an enrichment of GC content that permits the formation of secondary structures within the 3’UTR. Taken together, this study identifies a subset of protein-coding transcripts whose 3’-end processing requires the Integrator complex.

overall_design:
ChIP-seq of CPSF73, CSTF64 and H3K36me2 in INTS11-depleted HeLa shINTS11 cells in duplicates.
eCLIP in HeLa shINTS11 cells in duplicates.
3' mRNA-Seq in HeLa WT shINTS11 and E203Q shINTS11 cells in duplicates.

first: Lucas

last: Ferreira Da Silva

first: Ezra

last: Blumenthal

first: Pradeep

middle: R

last: Cingaram

first: Helena

last: Gomesdos Santos

first: Raghu

last: Edupuganti

first: Anda

last: Zhang

first: Sadat

last: Dokaneheifard

first: Yuki

last: Aoi

first: Jingyin

last: Yue

first: Mina

last: Tayari

first: Ali

last: Shilatifard

first: Ramin

last: Shiekhattar


title: Multi-omic approach identifies a transcriptional network coupling innate immune response to proliferation in the blood of COVID-19 cancer patients

city: rome

first: andrea

last: sacconi

address: via elio chianesi

country: Italy

institute: regina elena cancer institute

summary: Clinical outcomes of COVID-19 patients are worsened by the presence of co-morbidities, especially cancer for which mortality rate in cancer patients affected by COVID-19 is elevated. SARS-CoV-2 infection is known to alter immune system homeostasis. Whether cancer patients developing COVID-19 present alterations of immune functions which might contribute to worse outcomes has been so far poorly investigated. We conducted a multi-omic analysis of immunological parameters in COVID-19 patients with and without cancer. We found that 8 pro-inflammatory factors out of 27 analysed serum cytokines were modulated in COVID-19 patients irrespective of cancer status. Diverse subpopulations of T lymphocytes such as CD8+ T, CD4+ T central memory, Mucosal associated invariant T cells (MAIT) NKT and  T cells were reduced while B memory cells, plasmablasts, late NK and plasmacytoid dendritic cells were expanded in COVID-19 cancer patients. A 19 gene expression signature of peripheral blood cells was able to discriminate COVID-19 cancer and without cancer patients. Gene set enrichment analysis highlights an increased gene expression in Interferon  response and signalling which paired with aberrant cell cycle regulation in cancer patients. Ten out of these 19 genes were specific of COVID-19 cancer patients. Our findings illustrate a repertoire of aberrant alterations of gene expression in circulating immune cells of COVID-19 cancer patients that might contribute to decipher their higher frequency of severe events. We also unveil a transcriptional network involving gene regulators of both inflammation response and proliferation in PBMCs of COVID-19 cancer patients. This might also lead to design of novel therapeutic strategies for COVID-19 cancer patients.

overall_design: 12 PBMC samples were analyzed. 5 are COVID-19 patients, 5 are COVID-19 patients with cancer and 2 are healthy subjects.

first: Andrea

last: Sacconi

first: Giulia

last: Piaggio

first: Gennaro

last: Ciliberto


title: Tristetraprolin prevents gastric metaplasia by suppressing pathogenic inflammation

city: Durham

first: Perry

last: Blackshear

state: NC

address: 111 TW Alexander Drive

department: STL

institute: NIH/NIEHS

summary:
Purpose: The goals of this study are to examine whether TTP can protect the stomach from adrenalectomy (ADX)-induced gastric inflammation and spasmolytic polypeptide-expressing metaplasia (SPEM).
Methods: we utilized the TTP∆ARE mouse model to examine whether TTP overexpression can protect the stomach from adrenalectomy (ADX)-induced gastric inflammation and spasmolytic polypeptide-expressing metaplasia (SPEM).
Results:  We found that TTP∆ARE mice were completely protected from ADX-induce gastric inflammation and SPEM. RNA sequencing revealed that TTP overexpression suppressed the expression of genes associated with the innate immune response. Finally, we show that protection from gastric inflammation was only partially due to suppression of Tnf, a well-known TTP target.
Conclusions:  Our results demonstrate that TTP exerts broad anti-inflammatory effects in the stomach, and suggest that therapies that increase TTP expression may be effective treatments of pro-neoplastic gastric inflammation.

overall_design: RNA-seq analysis of TTP∆ARE and WT mouse stomachs

first: Jonathan

middle: T

last: Busada

first: Stuti

last: Kadka

first: Kylie

middle: N

last: Peterson

first: Deborah

middle: J

last: Stumpo

first: Lecong

last: Zhou

first: John

middle: A

last: Cidlowski


title: Role of Adipocyte Na,K-ATPase Oxidant Amplification Loop in Cognitive Decline and Neurodegeneration - Expression profiling in Brain

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

summary: Adipocyte-specific expression of Na,K-ATPase signaling antagonist, NaKtide, has been shown to ameliorate the pathophysiological consequences of obesity and improve diseased phenotype. Recent studies have established that the release of adipocytokines and other bioactive mediators in obesity contributes to neurodegeneration. This study  utilizes a mechanistic approach and characterizes the hippocampal transcriptome in comparison with transcriptomic changes in liver, visceral and subcutaneous adipose tissue. RNAseq analysis in high fat diet fed transgenic mice showed large scale differential gene expression as well as modulation of several biological pathways in hippocampus, liver, visceral and subcutaneous adipose tissue, which were attenuated by doxycycline induced adipocyte specific NaKtide expression.

overall_design: A total of 12 experimental conditions (three tissues: Liver, Visceral Adipose Tissue, and Subcutaneous Adipose Tissue; two diets: control diet and western diet; and two treatments: NaKtide and control) were compared. Five mice were placed in each experimental group for a total of 60 samples. Total RNA was extracted and used for expression profiing by RNA-Seq in a 2x50bp paired-end design.

first: Komal

last: Sodhi

first: Rebecca

last: Pratt

first: Xiaoliang

last: Wang

first: Mishghan

last: Zehra

first: Jiayan

first: Lawrence

last: Grover

first: Brandon

last: Henderson

first: Donald

last: Primerano

first: Jun

last: Fan

first: Jiang

last: Liu

first: Thomas

last: Nelson

first: Joseph

last: Shapiro


title: Role of Adipocyte Na,K-ATPase Oxidant Amplification Loop in Cognitive Decline and Neurodegeneration

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: RNA-Seq analysis of classical monocyte in pateints with sickle cell disease [RNA-Seq]

city: New York

first: Yunfeng

state: NY

address: 310 East 67th Street

department: Lindsley F. Kimball Research Institute (LFKRI)

institute: New York Blood Center

summary: Patients with sickle cell disease (SCD) suffer from intravascular hemolysis associated vascular injury and tissue damage. Classical monocytes (CMo), which comprise most blood circulating monocytes. are activated in SCD, but the cause and consequences of activation is less clear. Using transcriptome analysis, we found upregulation of the type I Interferon (IFN) pathway in sort-purified SCD CMo.

overall_design: CD14+CD16- classical monocyte were purifed with CD14 microbeads and sorted with flow cytometer

first: Karina

last: Yazdanbakhsh


title: Temporal expression study of microRNAs in crown tissues of winter wheat grown under natural growth condition

city: Xinxiang

first: Miao

last: Zhao

state: Henan

address: Jianshe east road

department: Life sciences college

country: China

institute: Henan Normal University

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are single strand small non-coding RNAs that regulate target mRNAs at post-transcription level. Winter wheat (Triticum aestivum L.), is an important crop plant all over the world. Long term cold exposure (vernalization) is necessary for winter wheat transition from vegetative growth to reproductive growth, yet the involvement of miRNAs in these stages remains unknown. Therefore, we performed next generation sequencing of small RNAs profiles in crown tissues at three-leaf stage, winter dormancy stage, spring greenup stage and jointing stage.

overall_design: To identify miRNAs involved in winter wheat growth and development in te field, winter wheat cultivar Shimai 22 was grown in the field under natural weather condition. Crown tissues were collected at 4 different growth and development stages: three leaf stage, winter dormancy stage, spring greenup stage and jointing stage, small RNA libraries were constructed, and BGISEQ500 RS (BGI, China) sequencing platform was used for small RNA libraries sequencing.

first: Yong-Fang

last: Li


title: DNA G-quadruplexes in human stem cells and during differentiation

first: Angela

last: Simeone

summary: The establishment of cell identity involves the activation of developmental gene expression programs and is underpinned by epigenetic factors including DNA methylation and histone modifications. G-quadruplex DNA secondary structures (G4) are genomic elements implicated in transcriptional regulation, genome instability and cancer. We reasoned that G4s might be central features that influence development. In human embryonic stem cells G4s are highly abundant and progressively lost during differentiation. They are prevalent in enhancers and promoters and their inheritance is linked to transcriptional stabilisation of key homeostasis genes and to transitions in the histone modification landscape. Interventional G4 stabilisation by a small molecule leads to developmental delay. Our findings suggest that G4s are epigenetic marks involved in stem cell pluripotency and differentiation.

overall_design: DNA G-quadruplexes (G4-ChIP-seq), accessibility (ATAC-seq) and gene expression have been profiled in three stem cells:  H9 human embryonic stem cells (ESC), H9-derived cranial neural crest cells (CNCCs) and in H9-derived neural stem cells (NSC).  For G4-ChIP-seq 3 biological replicates have been performed, and each of those have been assessed by 3 technical replicates and 1 input library.Three biological replicates per cell type for ATAC-seq were performed. Furthermore, 5 biological replicates for ESC, 3 biological replicates for CNCC, 4 biological replicates for NSC were performed for RNA-seq.

first: Katherine

last: Zyner

first: Santosh

last: Adhikari

first: David

last: Tannahill

first: Shankar

last: Balasubramanian


title: Integrated molecular analysis identifies new developmental pericyte markers in zebrafish

city: Worcester

first: Nathan

middle: D.

last: Lawson

address: 364 Plantation Street

department: Molecular, Cell, and Cancer Biology

institute: University of Massachusetts Medical School

summary: We performed single cell and bulk RNA-seq analyses on pdgfrb-positive cells to identify candidate pericyte-expressed genes. For bulk RNA-seq, we used wild type pdgfrb-positive samples from Series GSE152759 (GEO ID: GSM4625924, GSM4625925, GSM4625926) for comparison to mutant pdgfrb-positive cells in this Series. These cells had originally been isolated in parallel.

overall_design: RNA-seq was performed on transgene-positive cells isolated by FACS.


title: A Positive Feedback Loop Between TGFβ and Androgen Receptors Supports Triple-Negative Breast Cancer Anoikis Resistance

city: Salt Lake CIty

first: Jason

last: Gertz

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

summary: Triple-negative breast cancer (TNBC) is an aggressive subtype with few treatment options for chemo-resistant disease. In both preclinical models and patient circulating tumor cells, androgen receptor (AR) expression is increased in anchorage independent TNBC. The AR inhibitor enzalutamide (Enza) leads to reduced TNBC growth in soft agar, invasion, mammosphere formation in vitro, and reduced tumorigenicity and recurrence when combined with chemotherapy in vivo pre-clinical models. Transforming growth factor β (TGFβ) pathway gene signatures are also increased during TNBC anchorage independent survival both in vitro and in vivo in pre-clinical models and CTC from patients during relapse while on chemotherapy. We hypothesized that a positive loop between AR and TGFβ signaling facilitates TNBC anchorage independent survival (anoikis resistance). We previously published that AR protein levels and transcriptional activity increased during anchorage independent conditions and we now find that that multiple components of the TGFβ pathway, including TGFβ1 and 3, as well as pathway activity, as measured by nuclear localization and transcriptional activity of pSmad3, are enhanced in anchorage independent conditions. Indeed, exogenous TGFβ increased AR protein and TGFβ inhibition decreased AR and TNBC viability, particularly under anchorage independent culture conditions. ChIP-Seq experiments revealed AR binding to genomic regions near the TGFB1 and SMAD3. TGFB3 and AR expression were positively correlated in clinical datasets and high levels of co-expression correspond to significantly worse recurrence-free and overall survival in both ER- and basal-like breast cancer. Finally, combining Enza with a TGFβ inhibitor decreased cell survival more than either drug alone, particularly under anchorage independent conditions, where the effect was more than additive. These findings warrant further investigations into whether combined inhibition of AR and TGFβ pathways might decrease metastatic recurrence rates and mortality from TNBC.

overall_design: ChIP-seq of androgen receptor in MDA-MB-453 attached and suspension cultures treated with dihydrotestosterone and enzalutamide.

first: Emmanuel

last: Rosas

first: Jeffery

last: Vahrenkamp

first: Jennifer

last: Richer


title: Total and AGO1 immuniprecipitated small RNA from Arabidopsis thaliana WT and ago1-57 mutant, mock and TuYV infected rosette leaves

city: Strasbourg cedex

first: Pascal

last: Genschik

address: 12, rue du général Zimmer

country: France

institute: Institut de biologie moléculaire des plantes

summary: In plants and some animal lineages, RNA silencing is an efficient and adaptable defense mechanism against viruses. To counter it, viruses encode suppressor proteins that interfere with RNA silencing. Phloem-restricted viruses are spreading at an alarming rate and cause substantial reduction of crop yield, but how they interact with their hosts at the molecular level is still insufficiently understood. Here, we investigate the antiviral response against phloem-restricted turnip yellows virus (TuYV) in the model plant Arabidopsis thaliana. Using a combination of genetics, deep sequencing, and mechanical vasculature enrichment, we show that the main axis of silencing active against TuYV involves 22-nt vsiRNA production by DCL2, and their preferential loading into AGO1. Moreover, we identify vascular secondary siRNA produced from plant transcripts and initiated by DCL2-processed AGO1-loaded vsiRNA Unexpectedly, and despite the viral encoded VSR P0 previously shown to mediate degradation of AGO proteins, vascular AGO1 undergoes specific post-translational stabilization during TuYV infection. Collectively, our work uncovers the complexity of antiviral RNA silencing against phloem-restricted TuYV and prompts a re-assessment of the role of its suppressor of silencing P0 during genuine infection.

overall_design: 8 samples examinated: Arabidopsis thaliana total and AGO1 IP small RNA from Col-0 WT leaves and ago1-57, mock inoculated (2 biological replicates each). Arabidopsis thaliana total and AGO1 IP small RNA from Col-0 WT leaves and ago1-57, TuYVs81 infected. (2 biological replicates each).

first: Marion

last: Clavel

first: Esther

last: Lechner

first: Marco

last: Incarbone

first: Timothée

last: Vincent

first: Valerie

last: Cognat

first: Ekaterina

last: Smirnova

first: Véronique

last: Brault

last: Ziegler-Graff


title: Effect of maternal iron deficiency on placental gene expression on gestational day 18.5 in rats

city: London

first: Stephen

last: Renaud

state: Ontario

address: 1151 Richmond St, MSB428

country: Canada

institute: University of Western Ontario

summary: Iron deficiency occurs when iron demands chronically exceed intake, and is particularly prevalent in pregnant women. Iron deficiency during pregnancy poses health risks for the baby. The placenta serves as the interface between a pregnant mother and her baby; thus, maternal iron deficiency may indirectly impact fetal growth and development by altering placental function. In this study, pregnant Sprague-Dawley rats were fed either a low-iron or iron-replete diet starting two weeks before mating. On gestational day 18.5, RNA was collected, and a Clariom S microarray was performed to elucidate differences in gene expression between gestaional day 18.5 placentas isolated from dams fed iron replete or iron deficient diets.

overall_design: Two weeks before mating, female rats were randomly assigned either to a control diet group (37 mg/kg iron) or an iron-restricted diet group (3 mg/kg iron diet). After 2 weeks, female rats were bred to age-matched males fed a standard rodent chow. Dams in the control group were maintained on the same control diet throughout pregnancy; dams on the iron-restricted diet were transferred to a diet that contained 10 mg/kg iron for the duration of the study. On GD18.5, placentas were isolated, RNA extracted using a TRIzol-RNeasy column hybrid protocol including on-column DNase I digestion, and purified. Each sample represents RNA pooled from 2 placentas from a single dam. Normalization and output file generation was performed with Affymetrix Gene Expression Console (Thermo) using the Robust Multi-Chip Analysis (RMA) algorithm [RMA-Gene-full].

first: Hannah

last: Roberts


title: Role of Adipocyte Na,K-ATPase Oxidant Amplification Loop in Cognitive Decline and Neurodegeneration - Expression profiling in Liver and Fat

first: James

last: Denvir

first: Komal

last: Sodhi

first: Rebecca

last: Pratt

first: Xiaoliang

last: Wang

first: Mishghan

last: Zehra

first: Jiayan

first: Lawrence

last: Grover

first: Brandon

last: Henderson

first: Donald

last: Primerano

first: Jun

last: Fan

first: Jiang

last: Liu

first: Thomas

last: Nelson

first: Joseph

last: Shapiro


title: Genome wide chromatin changes in Wild Type and DDX5 knockdown of GC cells [RNA polymerase II ChIP-seq]

city: Jinan

first: Yan

last: Zheng

state: Shandong

address: No.440 Jiyan road

department: Shandong Provincial Key Laboratory of Radiation Oncology

institute: Shandong Cancer Hospital Affiliated to Shandong University

summary: DDX5 (DEAD-Box Helicase 5) plays a role as an adaptor molecule, is involved in a variety of cellular processes. Here, we performed ChIP-seq with antibody specific for RNA Polymerase II in HGC-27 cells after transduction with lentivirus harboring DDX5 shRNA or non-targeting shRNA.

overall_design: Two samples were examined: HGC-27 cells transduced with lentivirus harboring DDX5 shRNA or non-targeting shRNA.

first: Ming

last: Yang


title: Next Generation Sequencing Facilitates Quantitative Analysis of Hedgehog Signaling Blockade on Macrophage Transcriptomes

city: Birmingham

first: Dongquan

last: Chen

state: AL

address: 1717 11th Ave South

department: Medicine

institute: Univ of Alabama at Birmingham

summary: Purpose:  The goal of this study is to compare transcriptome profiling (RNA-seq) between macrophages inhibited for Hedgehog signaling and vehicle control.

overall_design: Methods: mRNA-sequencing was performed on the Illumina HiSeq2500 of macrophages in the presence or absence of a hedgehog inhibitor.

first: Ann

last: Hanna


title: Epigenetic Signature of Chronic Low Back Pain in Human T Cells

city: Minneapolis

first: Laura

middle: S

last: Stone

state: MN

address: 420 Delaware Street SE, MMC 294

department: Anesthesiology

institute: University of Minnesota

type: Methylation profiling by genome tiling array

summary: We performed genome-wide DNA methylation analysis of 850,000 CpG sites in women and men with chronic Low Back Pain (LBP) and pain free-controls. T cells were isolated (Discovery Cohort, n=32) and used to identify differentially methylated CpG sites, and gene ontologies and molecular pathways were identified.T cells were isolated (Discovery Cohort, n=32) and used to identify differentially methylated CpG sites, and gene ontologies and molecular pathways were identified. A polygenic DNA methylation score for LBP was generated in both women and men. Validation was performed in an independent cohort (Validation Cohort, n=63) of chronic LBP and healthy controls. Analysis with the Discovery Cohort revealed a total of 2,496 and 419 differentially methylated CpGs in women and men, respectively. The majority of these sites were hypo-methylated in women and enriched in genes with functions in the extracellular matrix, the immune system (i.e. cytokines) or in epigenetic processes. In men, we identified a unique chronic LBP DNA methylation signature characterized by significant enrichment for genes from the major histocompatibility complex. A sex-specific polygenic DNA methylation score was generated to evaluate the pain status of each individual and confirmed in The Validation Cohort using pyrosequencing.

overall_design: CD3+ T cells were isolated, DNA was isolating and bisulfite conversion was performed. DNA methylation profiles were generated using Illumina® 850 K bead arrays (Infinium MethylationEPIC Kit).

first: S

last: Grégoire

first: D

last: Cheishvili

first: M

last: Salmon-Divon

last: Dymov

first: L

last: Topham

first: V

last: Calderon

first: Y

last: Shir

last: Szyf


title: Transcriptomes of control and Chd7-deficient spiral ganglia neurons and cochlear hair cells

first: Mohi

last: Ahmed

address: Great Maze Pond

institute: King's College London

summary: The aim of this study is to identify the gene targets of Chd7 (by RNA-seq) in spiral ganglia neurons and cochlear hair cells. mRNA profiles of FACS-sorted spiral ganglia neurons from 4-day old mice and cochlear hair cells from embryos af 16.5 days in controls, Chd7 heterozygous and Chd7 homozygous mutant animals were generated by paired-end sequencing, in triplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were reads were aligned to mouse MM10 genome assembly using HiSAT2 (version 2.1.0) with the default parameters in Galaxy (version 2.1.0). To facilitate quantitative gene expression analysis, aligned reads for each sample were counted using featureCounts (version1.6.4). Differential gene expression analysis was performed using DESeq2 (version 2.11.40.6), applying parametric fit. qRT–PCR validation was performed using SYBR Green and gene specific primers. To identify differentially expressed genes, RPKM values of genes that are not normally expressed in E16.5 hair cells or P4 spiral ganglia neurons were removed from analysis. This resulted in 6910 transcripts for genes expressed in hair cells and 11293 genes expressed in neurons. A pairwise comparison between controls and homozygotes and controls and heterozygotes was performed. Significant thresholds were considered for transcripts with an adjusted p-value (FDR) of ≤0.05 and linear fold change of >2 in either direction. Altered expression of selected genes was confirmed with qRT–PCR as well as the encoded proteins by immunohistochemistry. Analysis of differentially expressed genes uncovered novel targets and potential mechanisms by which Chd7 controls the survival of these cells during normal hearing.

overall_design: Hair cell mRNA profiles of embryonic day (E) 16.5 Atoh1Cre;mTmG control (CTRL), Atoh1Cre;Chd7f/+;mTmG heterozygous (HET) and Atoh1Cre;Chd7f/+;mTmG heterozygous (HOM) mice. Neuronal mRNA profiles of 4-day old NeuroD1Cre;mTmG control (CTRL), NeuroD1Cre;Chd7f/+;mTmG heterozygous (HET) and NeuroD1Cre;Chd7f/+;mTmG heterozygous (HOM) mice.

first: Ruth

last: Moon

first: Andrea

last: Streit


title: Four-month-old zebrafish brain transcriptome analysis of mitofusin 2 (mfn2) loss-of-function mutation (hu3528 allele) homozygous, heterozygous, and wild type siblings

city: Adelaide

first: Lachlan

last: Baer

address: North Terrace

country: Australia

institute: The University of Adelaide

summary: An assessment of brain transcriptome differences between zebrafish siblings homozygous, heterozygous, and wild type for a loss-of-function mutation in mfn2.

overall_design: Six families of siblings were generated by mating of pairs of zebrafish heterozygous for the hu3528 allele of the mfn2 gene (https://doi.org/10.1371/journal.pone.0067276). Each family was raised from a single mating event. Each family was derived from a different pair of heterozygous fish. The mfn2 homozygous mutant fish have lower fitness than other genotypes and so, at 2.5 months of age, the siblings of a family were genotyped using PCRs on DNA from tail biopsies, and then separated into wild type, homozygous and heterozygous groups that were subsequently raised in separate tanks in the same recirculated water system. At 4 months of age the fish were humanely euthanised using tricaine and their brains were removed for RNA purification. The brains of two male and two female fish from each tank were pooled before RNA purification of total RNA using Trizol (Invitrogen) and Direct-Zol (Zymo Research). RNA-seq was performed on the Illumina HiSeq platform (Illumina, San Diego, California, USA) by Novogene (UK) Company Limited, Cambridge, UK. Libraries were provided as paired-end (2x150bp) reads for n = 6 from each of the three genotypes. Library sizes ranged between 40,530,508 and 69,496,372 reads.

first: Michael

last: Lardelli

first: Andrew

last: Grierson

first: Stephen

last: Pederson


title: Immune activation in the brains of fetal and adolescent mice

city: Guangzhou

first: Xinping

last: Yang

state: Guangdong

address: 1838 N. Guangzhou Ave

institute: Southern Medical University

summary: In order to investigate how the immune genes might be involved in the molecular mechanism underlying schizophrenia, we induced immune activation twice in mice, first time during mid-late fetal development stage by intraperitoneal injection (IPI) of lipopolysaccharide (LPS) in to the pregnant mice at G16 (16th day after gestation) and second time during puberty by IPI of LPS into the male offspring at P30 (30th day after birth), and carried out poly-A selected RNA-seq sequencing on the brain at P32 to evaluate transcriptional changes. We used saline as control for LPS, and set the experiments in three combination of saline and LPS treatments: (1) S-S (control group): saline at G16 + saline at P30; (2) L-S: LPS at G16 + saline at P30; (3) S-L: saline at G16 + LPS at P30; (4) L-L: LPS at G16 + LPS at P30.

overall_design: To explore the  effects of 4 treatments on the brain development of mice.

first: Yue

last: Gao

first: Shuangyan

last: Li

first: Yanjun

first: Xiaozhen

last: Liang

first: Bing

last: Zhang


title: Transcriptome high-throughput sequencing derived from mouse blastocysts with artificial oocyte activation treatment

city: 黄浦区

first: yin

last: mingru

state: 上海市

address: 上海市黄浦区制造局路639号

institute: 上海交通大学医学院附属第九人民医院

summary: Intracytoplasmic sperm injection (ICSI) has been an effective infertility treatment. Nevertheless, ICSI failures still occurred. One of the factors associated with ICSI failure is oocyte activation deficiency (AOD). The most commonly applied method of artificial oocyte activation (AOA) in humans includes ionophore. Although AOA is performed as a routine process in many assisted reproduction centers, up to date, there is no relevant study to expound whether AOA procedures increase developmental risks by disturbing subsequent gene expression during the embryonic development stages. Our results for the first time provide a profile of the changes in the global patterns of gene expression in AOA treatment versus ICSI generated mouse early embryos. In particular, we focus on the expression changes of imprinted genes. Another key observation in this study is that AOA treatment affects imprinted gene Igf2r expression and mehtylation, which is regulated by the imprinted Airn macro long non-coding (lnc) RNA.

overall_design: Three groups and three independent replicates for each treatment procedure were collected. ICSI, ICSI-AOA and dICSI-AOA were named group A, B and D, respectively in the following sequencing. Group A was the control group.

first: mingru

last: yin

first: weina

last: yu


title: Discrete Adaptive Responses to MEK Inhibitor In Subpopulations of Triple-Negative Breast Cancer [RNA-seq]

city: Cambridge

first: Daniel

middle: Robert

last: Goulet

address: 500 Main St

department: Koch Institute

institute: Massachusetts Institute of Technology

summary: We characterize gene expression in epithelial and mesenchymal subpopulations isolated from a triple-negative breast cancer cell line in response to trametinib treatment.

overall_design: We isolated EpCAM+ CD49f+ (POS) and EpCAM- CD49f- (NEG) isolated subpopulations by FACS, then performed RNA-seq following treatment as indicated


title: CBFβ promotes colorectal tumor growth and metastasis in a RUNX2-dependent manner (ChIP-seq)

city: Nanjing

first: chen

last: Wang

address: xianlin street num 163

institute: Nanjing University

summary: Transcriptional regulation is critically involved in colorectal cancer (CRC) pathogenesis, the mechanism of which remains incompletely understood. Here, we report that core-binding factor β (CBFβ) is commonly upregulated in human colorectal cancer and is associated with the survival rate of CRC patients. Immunohistochemistry (IHC) analysis of RUNX1-3 expression in CRC patients and other in vitro data revealed that CBFβ promotes cell proliferation and liver metastasis in a RUNX2-dependent way. Transcriptome sequencing, ChIP-seq and promoter-binding experiments demonstrated that the CBFβ/RUNX2 complex could activate the transcription of OPN, FAM129A and UPP1. Furthermore, CBFβ significantly promoted tumor growth and lung metastasis in a mouse xenograft model and an orthotopic liver metastasis model of CRC.  Additionally, we identified that tumor-suppressive miR-143/145 could synergistically target CBFβ by specifically binding to its 3’-UTR region. An inverse correlation between miR-143/145 and CBFβ was verified in CRC patients. Our results represent the first report describing a mechanistic role for CBFβ-RUNX2 in the transcriptional activation of OPN, FAM129A and UPP1 in controlling colorectal cancer development, which may offer prognostic and therapeutic opportunities.

overall_design: ChIP-seq analysis for RUNX2 to identify the genes that are directly regulated by RUNX2 at the transcriptional level

first: Chen

first: Yuqian

first: Ziyu

last: Shi

first: Mingyue


title: Low-input, deterministic profiling of single-cell transcriptomes reveals individual intestinal organoid subtypes comprised of single, dominant cell types [Dispencell]

city: Lausanne

first: Marjan

last: Biočanin

state: Vaud

address: Station 19, SV 3820

department: SV-IBI

country: Switzerland

institute: EPFL

summary: High-throughput single-cell RNA-sequencing (scRNA-seq) has transformed our ability to resolve cellular properties across systems. A key scRNA-seq catalyzer was the introduction of microdroplet-based systems, which vastly improved sample handling and cell throughput. While powerful, the current microfluidic systems are limited to high cell density (>1000 cells) samples. This prevents the efficient processing of individual, small tissues or rare cells, leading to respectively confounded mosaic cell population read-outs or failed capture of diagnostically interesting cells.  In this study, we developed a deterministic, mRNA-capture bead and cell co-encapsulation droplet system, DisCo, that overcomes these limitations by enabling precise particle position and droplet sorting control through combined machine-vision and multilayer microfluidics. We demonstrate that DisCo is capable of processing samples containing few cells (< 100 cells) at high efficiencies( >70%). To underscore the unique capabilities of DisCo, we mapped the developmental process of 31 individual intestinal organoids at the single cell level. This uncovered extensive cellular heterogeneity among organoids, revealing two so far uncharacterized organoid subtypes, “gobloids” and spheroids, predominantly consisting of respectively Muc2+ goblet and Ly6a+ stem cells. Further Disco data analysis thereby revealed strongly increased Yap1 target gene expression in these spheroids, suggesting mechano sensing as the underlying mechanism for their spontaneous formation.  Together, our novel “no-cell-left-behind” platform enables the deterministic processing of input cells, allowing high-resolution snapshots of cellular heterogeneity among rare cells or individual, small tissues or organoids.Together, our novel “no-cell-left-behind” platform enables the deterministic processing of input cells, allowing high-resolution snapshots of cellular heterogeneity among rare cells or individual, small tissues or organoids.

overall_design: To benchmark single-cell recovery efficiencies throughout the complete DisCo workflow, we sorted HEK 293T cells utilizing the Dispencell pipetting robot. Cells were then processed with DisCo and libraries were prepared in order to quantify cell recovery efficiencies.

first: Johannes

last: Bues

first: Joern

last: Pezoldt

first: Riccardo

last: Dainese

first: Saba

last: Rezakhani

first: Wouter

last: Salen

first: Revant

last: Gupta

first: Esther

last: Amstad

first: Manfred

last: Claassen

first: Matthias

last: Lutolf

first: Bart

last: Deplancke


title: Low-input, deterministic profiling of single-cell transcriptomes reveals individual intestinal organoid subtypes comprised of single, dominant cell types [SPM]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: For benchmarking single-cell purity and doublet numbers in the DisCo platform, HEK 293T  and murine brown preadipocyte cells (iBA) were used.  Cells were mixed in a 1:1 ratio, adjusted to 20 cells/µl, and re-suspended in a cell buffer containing PBS, BSA, and Optiprep previous to loading onto the DisCo chip.


title: Low-input, deterministic profiling of single-cell transcriptomes reveals individual intestinal organoid subtypes comprised of single, dominant cell types [organoids]

overall_design: Single intestinal organoids were processed at single-cell resolution using deterministic encapsulation of cells with mRNA capture beads.

first: Antonius

last: Chrisnandy


title: G9a deletion in female ES cells

city: Boston

first: Attila

last: Szanto

address: 185 Cambridge St.

department: Molecular Biology

institute: Massachusetts General Hospital

summary: G9a was deleted from female ES cells (16.7 Tsix +/TST) . The effects were analyzed by RNA-seq and ChIP-Seq comparing undifferentiated and differentiated states.

overall_design: Mouse embryonic stem cells are compared. Parental line (16.7 Tsix +/TST) and G9a knockout in undifferentiated (d0) state and after 10 days of differentiation (d10).


title: Bulk RNA of IL-4 and squalene treated MDM

status: Public on Nov 09 2021

city: Los Angeles

first: Zulema

middle: R.

last: Garcia

state: CA

address: 18033 Le Conte Ave 52-121, Center for Heath Sciences

institute: University of California, Los Angeles

summary: We performed bulk RNA-seq on squalene/M-CSF-treated macrophages to compute the fold change of genes in the squalene/M-CSF compared to M-CSF alone treated macrophages. We then looked at the distribution of the log fold changes in the skin-derived TREM2 (607 genes) and M2-like (709 genes) macrophage scRNA-seq signatures. We found that the TREM2 gene signature was more highly induced by squalene/M-CSF than the M2-like macrophage signature. In these squalene-induced macrophages, we found upregulation of several of the lipid metabolism and pro-inflammatory genes present in the skin-derived TREM2 macrophage gene signature.

overall_design: The study was performed in accordance with protocols approved by the institutional review board at University of California, Los Angeles. All patients provided written informed consent. Healthy donors were recruited from the University of California, Los Angeles. Peripheral blood mononuclear cells (PBMCs) from healthy donors were isolated from peripheral blood using a Ficoll-Paque (GE Healthcare) density gradient. Monocytes were isolated from PBMCs via positive selection with CD14 microbead (Miltenyi Biotec, cat# 130-050-201). Monocytes were seeded at 500,000 cells/well in a 24-well plate and differentiated in M-CSF (50 ng/ml) (R&D Systems, cat. # 216MC025/CF) for 5 day in RPMI with 10% FCS at 37°C. Macrophages were then stimulated with M-CSF (50 ng/ml) (R&D Systems, cat. # 216MC025/CF), IL-4 (20ng/mL) (Peprotech, cat. # 200-04), and squalene (1 mM) (Thermofisher Scientific, cat.# S3626-100ML) for 1 days. RNA were extracted using Trizol RNA extraction protocol and Qiagen RNeasy Micro Kit . We quantified the RNA concentration and quality using TapeStation.

first: Tran

last: Do

first: Rosane

last: Teles

first: Alejandro

last: Espinoza

first: Robert

middle: L

last: Modlin


title: CBFβ promotes colorectal tumor growth and metastasis in a RUNX2-dependent manner

first: chen

last: Wang

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Differential gene expression in peripheral blood mononuclear cells from children immunized with inactivated influenza vaccine

city: PITTSBURGH

first: Uma

last: Chandran

state: PA

address: 5607 Baum Blvd

department: Biomedical Informatics

institute: University of Pittsburgh

summary: The human immune response to inactivated influenza vaccine is dynamic and impacted by age and preexisting immunity. Our goal was to identify postvaccination transcriptomic changes in peripheral blood mononuclear cells from children. Blood samples were obtained before and at 3 or 7 days postvaccination with 2016-2017 quadrivalent inactivated influenza vaccine and RNA sequencing was performed. There were 1,466 differentially expressed genes (DEGs) for the Day 0-Day 3 group and 513 DEGs for the Day 0-Day 7 group. Thirty-three genes were common between the two groups. The majority of the transcriptomic changes at Day 3 represented innate inflammation and apoptosis pathways. Day 7 DEGs were characterized by activation of cellular processes, including the regulation of cytoskeleton, junctions, and metabolism, and increased expression of immunoglobulin genes. DEGs at Day 3 were compared between older and younger children revealing increased inflammatory gene expression in the older group. Vaccine history in the year prior to the study was characterized by robust DEGs at Day 3 with decreased phagosome and dendritic cell maturation in those who had been vaccinated in the previous year. PBMC responses to inactivated influenza vaccination in children differed significantly by the timing of sampling, patient age, and vaccine history. These data provide insight into the expected molecular pathways to be temporally altered by influenza vaccination in children.

overall_design:
Transcriptomic analysis of blood cells from patients before influenza vaccination and at days 3 and 7 post vaccination.
>>> Submitter declares that the raw data are unavailable for privacy issues. <<<

first: John

middle: F

last: Alcorn

first: Richard

middle: K

last: Zimmerman


title: Next-Generation Sequencing Facilitates Quantitative Analysis of Wild Type and DDX5 knockdown of GC Transcriptomes

first: Yan

last: Zheng

summary: We aimed to detect the mRNA expression levels in HGC-27 cells after transduction with lentivirus harboring DDX5 shRNA or non-targeting shRNA.

overall_design: Totally, two samples were examined: HGC-27 cell transduced with lentivirus harboring DDX5 shRNA or non-targeting shRNA.

first: Ming

last: Yang


title: Next-Generation Sequencing Facilitates Quantitative Analysis of Wild Type and lncPSCA Overexpression of GC Transcriptomes

summary: We aimed to detect the mRNA expression levels in HGC-27 cells after transfection with lncPSCA expression plasmid or vector.

overall_design: Totally, two samples were examined: HGC-27 cell transfected with pcDNA3.1-lncPSCA, or pcDNA3.1.


title: m6A-mRNA & lncRNA Epitranscriptomic Microarray of HepG2 cells VS Fluid shear stress treated HepG2 cells

city: Chengdu

first: hongchi

last: Yu

state: Sichuan

address: No.24 South Section 1, Yihuan Road

institute: Sichuan University

type:
Non-coding RNA profiling by array
Expression profiling by array
Methylation profiling by array

summary: We conducted methylation microarray to investigate the post-transcriptional role of YAP in regulating EMT-related genes. Microarray profiling shows that 1062 transcripts are significantly hypermethylated and 2388 transcripts are significantly hypomethylated, which are associated with the gene expression in FSS-HepG2 cells. It indicates that HepG2 cells have a significantly changed methylation level after exposing to FSS.

overall_design: two samples. HepG2 cells used as control and Fluid shear stress treated HepG2 cells

first: Hongchi

first: Yang

last: Shen


title: CBFβ promotes colorectal tumor growth and metastasis in a RUNX2-dependent manner (RNA-seq)

overall_design: Significantly changed genes both in CBFβ-LV-HCT116 cells compared to the Control-LV-HCT116 cells and in shRNA-CBFβ-LV cells compared to the shRNA-Control-LV cells analyzed by RNA-seq

first: Chen

first: Yuqian

last: Zhang

first: Ziyu

last: Shi

first: Mingyue

last: Li


title: SAM Competitive PRMT5 Inhibitor PF-06939999 Demonstrates Antitumor Activity in Splicing Dysregulated NSCLC with Decreased Liability of Drug Resistance

city: San Diego

first: Tao

last: Xie

address: 10770 science Center Dr.

department: ORD

institute: Pfizer Inc

summary: Protein arginine methyltransferase 5 (PRMT5) over-expression in hematological and solid tumors methylates arginine residues on cellular proteins involved in important cancer functions including cell cycle regulation, mRNA splicing, cell differentiation, cell signaling, and apoptosis. PRMT5 methyltransferase function has been linked with high rates of tumor cell proliferation and decreased overall survival, and PRMT5 inhibitors are currently being explored as an approach for targeting cancer-specific dependencies due to PRMT5 catalytic function. Here we describe the discovery of potent and selective S-adenosylmethionine (SAM) competitive PRMT5 inhibitors, with in vitro and in vivo characterization of clinical candidate PF-06939999. Acquired resistance mechanisms were explored through the development of drug resistant cell lines. Our data highlight compound-specific resistance mutations in the PRMT5 enzyme that demonstrate structural constraints in the co-factor binding site that prevent emergence of complete resistance to SAM site inhibitors. PRMT5 inhibition by PF-06939999 treatment reduced proliferation of NSCLC cancer cells, with dose-dependent decreases in symmetric dimethyl arginine (SDMA) levels and changes in alternative splicing of numerous pre-mRNAs. Drug sensitivity to PF-06939999 in NSCLC cells associates with cancer pathways including MYC, cell cycle and spliceosome, and with mutations in splicing factors such as RBM10. Translation of efficacy in mouse tumor xenograft models with splicing mutations provides rationale for therapeutic use of PF-06939999 in the treatment of splicing dysregulated NSCLC.

overall_design: Quantification of RNA expression in cancer cells treated with PRMT5i (PF-06939999) vs. DMSO.

first: Kristen

last: Jensen-Pergakes

last: Tatlock

first: Karen

last: Maegley

first: Indrawan

last: McAlpine

first: Michele

last: McTigue

first: Christopher

last: Dillon

first: Yuli

first: Shinji

last: Yamazaki

first: Noah

last: Spiegel

first: Manli

first: Amy

last: Nemeth

first: Natalie

last: Miller

first: Eleanore

last: Hendrickson

first: Hieu

last: Lam

last: Sherrill

first: Chi-Yeh

last: Chung

first: Elizabeth

last: McMillan

first: Shannon

last: Karlicek Bryant

first: Prakash

last: Palde

last: Braganza

first: Alexei

last: Brooun

first: Ya-Li

last: Deng

first: Vesta

last: Goshtasbi

first: Susan

middle: E

last: Kephart

last: Kumpf

first: Wei

last: Liu

first: Ryan

last: Patman

first: Eugene

last: Rui

first: Stephanie

last: Scales

first: Michelle

last: Tran-Dube

first: Fen

first: Martin

last: Wythes

first: Thomas

last: Paul


title: Discrete Adaptive Responses to MEK Inhibitor In Subpopulations of Triple-Negative Breast Cancer [WES]

first: Daniel

last: Goulet

state: MA

type: Genome variation profiling by high throughput sequencing

summary: We report the genetic similarity of epithelial and mesenchymal subpopulations isolated from a triple-negative breast cancer cell line.

overall_design: We isolated EpCAM+ CD49f+ (POS) and EpCAM- CD49f- (NEG) isolated subpopulations by FACS, then performed whole exome sequencing of these isolated subpopulations.


title: Low-input, deterministic profiling of single-cell transcriptomes reveals individual intestinal organoid subtypes comprised of single, dominant cell types

first: Marjan

last: Biočanin


title: Cold-Responsive DPP4+ Progenitor Cells Facilitate Thermogenic Remodeling of Subcutaneous Adipose Tissue_isoproterenol treatment

city: Durham

first: Rana

last: Gupta

state: North Carolina

address: Carmichael Building, 300 North Duke St.

department: Duke Molecular Physiology Institute

institute: Duke University

summary: The physiological adaptation to cold environmental temperatures involves the remodeling of energy-storing white adipose tissue (WAT) into an energy-burning thermogenic phenotype, characterized by the emergence of multi-locular beige adipocytes.  To date, the full array of cold-responsive cells within WAT that mediate thermogenic remodeling remain undefined.  Here, we demonstrate that distinct perivascular PDGFRb+ adipocyte precursor cell (APC) subpopulations are differentially sensitive to cold temperatures in vivo. One day of cold exposure elicits striking transcriptional changes in DPP4+ PDGFRb+ APCs, whereas committed DPP4- PDGFRb+ preadipocytes appear comparatively much less responsive. This adaptation includes beta-adrenergic receptor mediated induction in the expression of the pro-thermogenic cytokine, IL-33.  DPP4+ PDGFRb+ cells represent the sole source of IL-33 within inguinal WAT of adult mice.  Doxycycline-inducible deletion of Il33 in PDGFRb+ cells at the onset of cold exposure significantly compromises the thermogenic remodeling of WAT without directly impacting the differentiation capacity of APCs per se.  Together, these studies reveal the presence of a cold-responsive progenitor cell subpopulation in adult WAT and highlight their ability to regulate tissue plasticity through the production of immunological factors.

overall_design: Bulk RNA-seq experiment to analyze gene expression profile of cultured inguinal primary white adipose tissue DPP4_neg APCs and DPP4_pos APCs treated with vehicle (PBS) or 10mM isoproterenol for 4 hours.

first: Bo

last: Shan

first: Mengle

last: Shao


title: Genome wide chromatin and transcriptome changes of Wild Type and DDX5 knockdown of GC cells

first: Yan

last: Zheng


title: Gene Regulation by ATF3 in response to serine deprivation

city: Augusta

first: Chunhong

last: Yan

state: GA

address: 1410 Laney Walker Blvd

department: Georgia Cancer Center

institute: Augusta University

summary: The goal of this study is to identify genes that are regulated by activiating transcription factor (ATF3) in the cellular response to serine deprivation. Serine biosynthesis is crucial for cancer cells to proliferate and survival under serine-limiting conditions. We found that ATF3 expression induced by serine deprivation supports cancer cell growth. This RNA-seq study is thus designed to understand how ATF3 regulates serine biosynthesis in cells. The results indicate that ATF3 regulates the genes involved in the serine synthesis pathway.

overall_design: ATF3-wildtype (wt) or -knockout (Ko) hTERT-RPE1 cells were cultured in the completed medium or serine/glycine-free medium for 8 h. Total RNAs were prepared from the cells and subjected to RNA-seq. There are 4 samples, each with a biological replicate. Therefore, Samples Wt0h1, Wt8h1, Ko0h1, and KO8h1 were from the same batch of treated cells, while Samples Wt0h2, Wt8h2, Ko0h2, and Ko8h2 were from a second batch of treated cells. These two batches of samples were from independent experiments carried out one week apart.

first: Xingyao

last: Li


title: Discrete Adaptive Responses to MEK Inhibitor In Subpopulations of Triple-Negative Breast Cancer [FAIRE-seq]

summary: We report the chromatin accessibility of epithelial and mesenchymal subpopulations isolated from a triple-negative breast cancer cell line.

overall_design: We performed FAIRE sequencing of NEG and POS isolated subpopulations treated with DMSO Control for 24 h or 30 nM trametinib for 24 h.


title: Resident macrophages in adult testis and epididymis originate from different waves of embryonic hematopoiesis

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Macrophages are principal immune cells of the epididymis and testis. Here we described that epididymal and testicular macrophages share core markers with tissue macrophages of other organs while concomitantly expressing a unique set of genes to perform organ specific functions.

overall_design: Analysis of the RNA expression in distinct organ derived macrophage.

first: Andreas

last: Schlitzer

first: Sudhanshu

last: Bhushan

last: Meinhardt

last: Ulas

first: Kristain

last: Handler


title: GABA-receptive microglia selectively sculpt developing inhibitory circuits

first: Emilia

last: Favuzzi

address: 220 Longwood Avenue, Armenise 217

department: Neurobiology

institute: Harvard Medical School

summary: Microglia, the resident immune cells of the brain, have emerged as crucial regulators of synaptic refinement and therefore wiring precision. However, whether the remodeling of distinct synapses during development is mediated by specialized microglia is unknown. Here, using in vivo two-photon imaging, we show that GABA-receptive microglia selectively interact with inhibitory synapses during a critical window of mouse postnatal development. GABA initiates a transcriptional synapse remodeling program within these specialized microglia, which in turn sculpt inhibitory connectivity without impacting excitatory synapses. Ablation of GABAB receptors within microglia impairs this process and leads to stereotyped repetitive behavior and hyperactivity. These findings demonstrate that distinct microglia differentially engage with specific synapse types during development.

overall_design: We performed single cell RNA sequencing (scRNA-seq) of microglia isolated from the somatosensory cortex of postnatal day 15 mice of the following genotypes: wild-type (Cx3cr1+/+; GABAB1Rfl/fl; N = 12; 3 females and 9 males; 2 replicates), Cre-Het controls (Cx3cr1Cre/+; GABAB1R+/+; N = 10; 8 females and 2 males; 1 replicate) and GABAB1R cKO (Cx3cr1Cre/+; GABAB1Rfl/fl; N = 13; 9 females and 4 males; 2 replicates). Single-cell RNA-seq libraries were prepared on the 10x Genomics platform and sequenced using the Nova-Seq 100 cycle kit (Illumina).

first: Giuseppe

last: Saldi

first: Gord

last: Fishell


title: Broad tropic zinc finger protein guided transcriptional activation of HIV

city: Duarte

first: Denis

last: OMeally

state: California

address: 1500 E Duarte Rd

department: Arthur Riggs Diabetes & Metabolism Research Institute

institute: City of Hope

summary: Human Immunodeficiency Virus type 1 (HIV-1) is a lentivirus that causes a persistent viral infection and results in the demise of immune regulatory cells. Clearance of HIV-1 infection by the immune system is inefficient, and integration of proviral DNA into the genome of host cells provides a means for evasion and long-term persistence. A therapeutic compound that specifically targets and sustainably activates a latent HIV provirus could be transformative and is an overarching goal for the “shock and kill” approach to a functional cure for HIV. Substantial progress has been made towards the development of recombinant proteins that can target specific genomic loci for gene activation, repression or inactivation by directed mutations. However, most of these modalities are too large, or too complex, for efficient therapeutic application. We describe here the development and testing of a novel recombinant zinc finger protein transactivator, ZFPb-362-VPR, which specifically and potently enhances proviral HIV transcription both in established latency models and across different viral clades. Additionally, ZFP-362-VPR activated HIV reporter gene expression in a well-established primary human CD4+ T-cell latency model and was specific in targeting the HIV LTR as determined from off-target transcriptome analyses. This study provides clear proof of concept for the application of a novel, and therapeutically relevant, protein transactivator to purge cellular reservoirs of HIV-1.

overall_design: To determine the extent to which ZFP-362-VPR and dCas9-VPR+sgF2-362 disrupted RNA expression, we compared pMo-HEK cells transfected with either construct to those transfected with a pcDNA3.1 control, each in quadruplicate.

first: Tristan

last: Scott

last: O’Meally

first: Nicole

last: Grepo

first: Citradewi

last: Soemardy

middle: C

last: Lazar

first: Yue

first: Marc

last: Weinberg

first: Vicente

last: Planelles

first: Kevin

middle: V

last: Morris


title: Activation of the Crtc2/Creb1 transcriptional network in skeletal muscle enhances weight loss during intermittent fasting

city: Jupiter

first: Jerome

last: Nwachukwu

state: Florida

address: 130 Scripps Way

department: Department of Immunology and Microbiology

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

summary: Exercise is a behavior modification indispensable for long-term weight loss. Exercise activates the Creb-Regulated Transcriptional Coactivator (Crtc) family of transcriptional coregulators to drive Creb1-mediated anabolic transcriptional programs in skeletal muscle. Here, we show that induced overexpression of a skeletal muscle specific Crtc2 transgene in aged mice leads to greater weight loss during alternate day fasting, and selective loss of fat rather than lean mass. Transcriptional profiling revealed that fasting and weight loss downregulated most of the mitochondrial electron transport genes and other regulators of mitochondrial function that were substantially reversed in the Crtc2 mice, which maintained higher energy expenditure during fasting. The Crtc2 mice displayed greater mitochondrial activity, metabolic flux capacity for both carbohydrates and fats, improved glucose tolerance and insulin sensitivity, and increased oxidative capacity before the fast, suggesting muscle-intrinsic mechanisms in support of improved weight loss. This work reveals that Crtc2/Creb1-mediated signaling coordinates metabolic adaptations in skeletal muscle that explain how Crtc2/Creb contribute to the effects of exercise on metabolism and weight loss.

overall_design: mice tibialis anterior muscles transduced with GFP (empty) or Crtc2 expression vector were compared by mRNA-seq after ad libitum feeding or 3 rounds of alternate day fasting (ADF)

first: Nelson

last: Bruno

first: Sathish

last: Srinivasan

first: Richard

last: Hawkins

first: David

last: Sturgill

first: Gordon

last: Hager

first: Stephen

last: Hurst

first: Shey-Shing

last: Sheu

first: Kendall

middle: W

last: Nettles

first: Michael

middle: D

last: Conkright


title: PRMT1-mediated FLT3 arginine methylation is required for maintenance of FLT3-ITD+ Acute Myeloid Leukemia

first: Xin

last: He

summary: The presence of FLT3-ITD mutations in patients with acute myeloid leukemia (AML) is associated with poor clinical outcome. FLT3 tyrosine kinase inhibitors (TKIs), although effective in kinase ablation, do not eliminate FLT3-ITD+ leukemia stem cells (LSCs) which are potential sources of disease relapse, prompting us to ask whether FLT3-ITD protein regulates the AML LSCs survival through a kinase-independent mechanism. Here, we show that expression of PRMT1, the primary type I arginine methyltransferase, significantly increases in LSC-enriched CD34+CD38- populations relative to normal counterparts. Genetic PRMT1 depletion blocked AML CD34+ cell survival, and had more potent effects in AML cells from patients harboring FLT3-ITD. Our genome wide analysis of gene expression and PRMT1 conditional KO mouse study confirmed that PRMT1 preferentially cooperates with FLT3-ITD contributing to AML cell maintenance. Mechanistically, PRMT1 catalyzed FLT3-ITD protein methylation at arginines 972/973, and PRMT1 promoted leukemia cell growth in a FLT3 methylation-dependent manner. Moreover, effects of FLT3-ITD methylation in AML cells were in part due to crosstalk with FLT3-ITD phosphorylation at tyrosine 969 (Y969). Importantly, FLT3 methylation persisted in FLT3-ITD+ AML cells following TKI (AC220) treatment, indicating that methylation occurs independently of kinase activity. Finally, in both patient-derived xenograft (PDX) and murine AML models, combined administration of AC220 with a type I PRMT inhibitor (MS023) enhanced elimination of FLT3-ITD+ AML relative to AC220 treatment alone. Our study demonstrates that PRMT1-mediated FLT3 methylation promotes LSC activity and suggests that combining PRMT1 inhibition with FLT3 TKI treatment could be a promising approach to selectively target FLT3-ITD+ LSCs.

overall_design: We want to explore whether PRMT1 function is more relevant to the pathogenesis of FLT3-ITD+ than that of FLT3-WT AML. To do so, we transduced two AML cell lines (MV4-11 and THP-1) plus one FLT3-ITD-transformed CB CD34+ cells along with shCtrl or shPRMT1 and performed RNA sequencing (RNA-Seq). Six Groups: Group1: FLT3-ITD+ CB cells transduced with lentiviral vector targeting non-silence squence (control ShRNA); Group2:FLT3-ITD+ CB  cells transduced with lentiviral vector containing interference squence targeting PRMT1  (PRMT1 shRNA); Group 3: MV4-11 cells transduced with lentiviral vector targeting non-silence squence (control ShRNA); Group 4: MV4-11 cells transduced with lentiviral vector containing interference squence targeting PRMT1 (PRMT1 shRNA);Group5: THP-1 cells transduced with lentiviral vector targeting non-silence squence (control ShRNA); Group6:THP-1  cells transduced with lentiviral vector containing interference squence targeting PRMT1  (PRMT1 SHRNA). Expression profiling data in PRMT1 KD FLT3-ITD+ Cord blood cells, MV4-11  and THP-1 cell lines were compared to corresponding control shRNA transduced cells by RNA-seq technology

first: Ling

last: Li

first: Juan

last: Du

first: Tae-Hyuk

last: Kang

first: Jinhui

last: Wang

first: Xiwei

last: Wu


title: IRF3-binding RNA RIP-seq

city: Shanghai

first: Junfang

last: Xu

address: 800 Xiangyin Road

institute: national key laboratory of medical immunology

summary: Flag-taged IRF3-binding RNAs were analyzed by imprinting RNA-sequencing of anti-flag antibody-retrieved complexes from macrophages lysate.

overall_design: Examination of IRF3-binding RNA from macrophages

first: Xuetao

last: Cao


title: Discrete Adaptive Responses to MEK Inhibitor In Subpopulations of Triple-Negative Breast Cancer [ChIP-seq]

first: Daniel

last: Goulet

summary: We characterize histone modifications and transcription factor binding by ChIP-seq in epithelial and mesenchymal subpopulations isolated from a triple-negative breast cancer cell line.

overall_design: We isolated EpCAM+ CD49f+ (POS) and EpCAM- CD49f- (NEG) isolated subpopulations by FACS, then performed ChIP-seq following treatment as indicated with the antibody as indicated.

middle: R

first: Joseph

middle: P

last: Foster II

first: Jon

last: Zawistowski

first: Samantha

middle: M

last: Bevill

first: Mélodie

last: Noël

first: José

last: Olivares-Quintero

first: Noah

last: Sciaky

first: Darshan

last: Singh

first: Charlene

last: Santos

middle: G

last: Pattenden

first: Ian

last: Davis

first: Gary

last: Johnson


title: Discrete Adaptive Responses to MEK Inhibitor In Subpopulations of Triple-Negative Breast Cancer

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Identification of differentially expressed genes that function  in early response to cold stress in Vitis amurensis

city: Beijing

first: Luming

last: Zou

state: PR

address: Haidian strict, Xiang Mountain South Road, Xiang Mountain South Village 20#

department: Institute of Botany

institute: University of Chinese Academy of Sciences

summary: We report the RNAseq technology for high-throughput profiling of differentially expressed genes after cold treatment in Vitis amurensis

overall_design: Examination of gene expression profiles in in vitro V. amurensis plants under control and cold stress conditions

first: Chong

last: Ren

first: Zhenchang

last: Liang


title: Cold-Responsive DPP4+ Progenitor Cells Facilitate Thermogenic Remodeling of Subcutaneous Adipose Tissue_p-CREB ChIP seq

first: Rana

last: Gupta

overall_design: ChIP-seq experiment to analyze phosphorylated-CREB DNA binding sites using ~1,000,000 primary white adipose tissue DPP4_pos APCs treated with vehicle (PBS) or 10mM isoproterenol for 4 hours.

first: Bo

last: Shan

first: Mengle

last: Shao


title: CaMK2D is a critical regulator of coactivation of leukemia stem cell factors in acute myeloid leukemia.

status: Public on Nov 08 2021

city: Hangzhou

first: Zhaoxing

last: Wu

state: State...

address: Jiefang Road 88, Hangzhou,  China

institute: Zhejiang university

summary: Relapse is one of the biggest challenges in treating acute myeloid leukemia (AML) due to leukemia stem cells (LSCs) resisting chemotherapy, providing a cellular reservoir to form the basis for relapse. Here, we identify CaMK2D is a critical regulator of stemness and leukemogenesis of AML. Transcriptionally, loss of CaMK2D was associated with down-regulation kinds of metabolic pathway of AML.

overall_design: mRNA profiles of molm13 cell line with control vector and CaMK2D-KO vector were generated by deep sequencing, using Illumina HiSeq 4000. In total, six samples were sequenced.

first: Rongzhen

last: Xu


title: FERONIA regulates plant growth and survival under salt stress by modulating the dark reversion of phyB via a signature of phosphorylation

city: shanghai

first: Xin

last: Liu

address: NO. 3888 Chenhua Road, Shanghai, China

institute: CAS Center for Excellence in Molecular Plant Sciences

summary: Here we report that FERONIA (FER) integrates phyB-mediated light signaling pathway to control salt stress response. Mutation in phytochrome B (phyB) largely suppresses the dwarfism and leaf bleaching phenotype of fer-4 mutant under salt stress. FER interacts with and phosphorylates the N-terminal domain of phyB. Mutation in fer-4 or disruption of the FER-mediated phosphorylation sites of phyB at Ser106 and Ser227 leads to a retention of phyB in the photobodies under dark conditions, suggesting that FER-mediated phosphorylation accelerates the dark reversion of phyB. Interestingly, salt stress slows down the dark reversion of phyB via the inhibition of the kinase activity of FER, and mutation of phyB or overexpression of PIF5 attenuates the salt-induced growth inhibition. Together, our study indicates that the plasma membrane-localized FER determines the dark reversion rate of phyB in the nucleus via a signature of phosphorylation and thus coordinates the extracellular stress signals and nuclear outputs to dynamically control plant growth and survival under stress conditions.

overall_design: mRNA profiles of 8-day old wild type (WT), fer and phybfer

first: Chunzhao

last: Zhao


title: Transcriptomic analysis of Brm-/- hematopoietic stem and progenitor cells (LSK)

city: Indianapolis

first: James

last: Ropa

state: IN

address: 950 W Walnut St

institute: Indiana University

summary: Little is known of hematopoietic stem (HSC) and progenitor (HPC) cell self-renewal. The role of Brahma (BRM), a chromatin remodeler, in HSC/HPC function is unknown. Bone marrow (BM) from Brm-/- mice manifested increased numbers of long- and short-term HSCs, GMPs, and increased numbers and cycling of functional HPCs. Brm-/- HSC/HPC show demonstrated functional differences compared to wildtype HSC/HPC in vivo and ex vivo, due in part to increased intracellular valine in lineage negative BM. To determine changes in gene programs associated with loss of BRM, we performed RNA sequencing on Brm-/- LSK cells. Brm-/- LSK exhibited upregulated interferon response/cell cycle gene programs, suggesting important extrinsic effects on primitive HSC/HPC from more mature HPC due to the absence of BRM.

overall_design: Bone marrow cells were harvested from wiltdype (n=3) or Brm-/- (n=3) mice. Lineage negative, CKIT+, SCA1+ (LSK) cells were sorted from each population using cell surface staining followed by flow cytometry. Cells were immediately lysed RNA was harvested and prepped for sequencing.

first: Hal

last: Broxmeyer


title: Human Reproduction is Regulated by Retrotransposons derived from Ancient Hominindae-Specific Viral Infections [RNA-seq]

city: Haining

first: Xinyu

last: Xiang

address: East Haizhou Road

department: Zhejiang University-University of Edinburgh Institute

institute: Zhejiang University

summary: Here, we report the transcriptome profile for dCAS9-KRAB CRISPRi targeting LTR5Hs in human primordial germ cell-like cells.

overall_design: There are 6 samples in total. For both CRISPRi-LTR5Hs (dCas9-KRAB with gRNAs targeting LTR5Hs) and CRISPRi-empty (dCas9-KRAB without gRNA) in hPGCLCs, three biological replicates were conducted.

first: Wanlu

first: Amander

last: Clark


title: Single-cell transcriptomics of cultured skeletal stem cells with a PDGFRbeta D849V mutation

city: Oklahoma City

first: Lorin

middle: E.

last: Olson

state: OK

address: 825 NE 13th St,

department: Cardiovascular Biology

institute: Oklahoma Medical Research Foundation

summary: We demonstrate that skeletal stem cells (SSCs) isolated from mice with a gain-of-function D849V point mutation in PDGFRbeta exhibit colony formation defects that parallel the wasting or overgrowth phenotypes of the mice. Single-cell RNA transcriptomics with SSC-derived polyclonal colonies was performed to characterize single-cell differentiation potential and molecular signatures. This study indicates multi-lineage potential of cultured SSCs and identifies molecular alterations in osteogenic and chondrogenic precursors.

overall_design: Single-cell RNA sequencing of sorted and cultured PDGFRalpha+/Sca-1+ skeletal stem cells of 3-weeks-old limb of four genotypes (STAT1+/-, STAT1-/-, PDGFRbD849V+/-STAT1+/-,PDGFRbD849V+/-STAT1-/-) of mice

first: Hae

last: Kwon


title: Cold-Responsive DPP4+ Progenitor Cells Facilitate Thermogenic Remodeling of Subcutaneous Adipose Tissue

summary: The physiological adaptation to cold environmental temperatures involves the remodeling of energy-storing white adipose tissue (WAT) into an energy-burning thermogenic phenotype, characterized by the emergence of multi-locular beige adipocytes.  To date, the full array of cold-responsive cells within WAT that mediate thermogenic remodeling remain undefined.  Here, we demonstrate that distinct perivascular PDGFRb+ adipocyte precursor cell (APC) subpopulations are differentially sensitive to cold temperatures in vivo. One day of cold exposure elicits striking transcriptional changes in DPP4+ PDGFRb+ APCs, whereas committed DPP4- PDGFRb+ preadipocytes appear comparatively much less responsive. This adaptation includes beta-adrenergic receptor mediated induction in the expression of the pro-thermogenic cytokine, IL-33.  DPP4+ PDGFRb+ cells represent the sole source of IL-33 within inguinal WAT of adult mice.  Doxycycline-inducible deletion of Il33 in PDGFRb+ cells at the onset of cold exposure significantly compromises the thermogenic remodeling of WAT without directly impacting the differentiation capacity of APCs per se.  Together, these studies reveal the presence of a cold-responsive progenitor cell subpopulation in adult WAT and highlight their ability to regulate tissue plasticity through the production of immunological factors.

overall_design: Bulk RNA-seq experiment to analyze gene expression profile in inguinal white adipose tissue DPP4_neg APCs and DPP4_pos APCs freshly isolated from male mice kept at room temperature (22°C) or exposed to cold (6°C) for 24 hours.


title: The anti-fibrotic drug pirfenidone inhibits liver fibrosis by targeting glrx

city: Wuhan

first: Yue

last: Xi

state: Hubei

address: 81 St

department: College of life sciences

institute: Wuhan University

summary: Purpose: The goals of this study are to compare transcriptomes of mouse primary HSCs treated with PFD or vehicle by RNA-seq

overall_design: Methods:  RNA-seq analysis of primary mouse HSCs treated with PFD one day after isolation and culture-activated for additional four days.

first: Wen

last: Xie

first: Sihan

last: Li


title: Vaccine-elicited CD4 T cells prevent the deletion of antiviral B cells in chronic infection

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

institute: University of Basel

summary: Vaccination induced CD4 T cells prevent B cell decimation by turning on a germinal center like transcriptional program. This cellular differentiation is similiar to the one observed when type I interferon receptor-deficient (IFNAR-/-) instead of wt mice are used as recipients.

overall_design: Analysis of KL25HL B cells recovered from LCMV-infected wt mice with either one of two forms of pre-existing CD4 T help (LM61 pre-immunization or  SM CD4 T cell adoptive transfer) or no pre-existing T help wt mice (LM immunization) or KL25HL B cells recovered from IFNAR-/- mice without pre-existing CD4 T help.

first: Kerstin

last: Narr

first: Florian

last: Geier

first: Daniel

last: Pinschewer


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Otud1-/- distal colonic Transcriptomes

status: Public on Nov 07 2021

city: beijing

first: Tongtong

address: Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing

institute: Peking University

summary: Conclusion: Otud1 knock out mice are less sensitive to DSS (Dextran sulfate) induced colitics

overall_design: WT C57BL/6 male mice and Otud1 knockout C57BL/6 male mice were fed with 1.5% DSS (Dextran sulfate) for 7 days. Then distal colon was taken out and the RNA is extracted by Trizol method, followed by eukaryotic RNA-seq and associated analysis

first: Fuping

last: You


title: TFAM-dependent mitochondrial metabolism is required for alveolar macrophages maintenance and homeostasis

city: ROCHESTER

first: Xiaochen

last: Gao

state: MN

address: 200 first street SW

department: Immunology

institute: Mayo Clinic

summary: In this report, we showed that TFAM deficiency caused impaired AM mitochondrial fitness, altered metabolism and defective lipid catabolic responses, leading to diminished AM quantity and altered AM phenotypes. We demonstrated that TFAM deficiency did not impair AM differentiation from their precursors, but caused reduced AM maintenance. RNA-seq experiment revealed that TFAM deficiency caused impaired AM self-renewal capability. We showed that TFAM deficiency in AMs caused impaired clearance of respiratory debris, surfactant and enhanced susceptibility to severe influenza virus infection. Finally, we found that influenza infection resulted in disruption of TFAM-mediated mitochondrial fitness and metabolism in AMs.

overall_design: Examined with bulk WT or TFAM-deficient AM

first: Jie

last: Sun


title: Evolution of Natural Lifespan Variation and Molecular Strategies of Extended Lifespan

city: Richmond

first: Alaattin

last: Kaya

state: VA

address: 1000 West Carry St, Room 126

department: Biology

institute: Virginia Commonwealth University

summary: Here, we analyzed 76 ecologically diverse wild yeast isolates and discovered a wide diversity of replicative lifespan. Phylogenetic analyses pointed to genes and environmental factors that strongly interact to modulate the observed aging patterns. We then identified genetic networks causally associated with natural variation in replicative lifespan across wild yeast isolates, as well as genes, metabolites and pathways, many of which have never been associated with yeast lifespan in laboratory settings. In addition, a combined analysis of lifespan-associated metabolic and transcriptomic changes revealed unique adaptations to interconnected amino acid biosynthesis, glutamate metabolism and mitochondrial function in long-lived strains. Overall, our multi-omic and lifespan analyses across diverse isolates of the same species shows how gene-environment interactions shape cellular processes involved in phenotypic variation such as lifespan.

sample_organism:
Saccharomyces cerevisiae
Saccharomyces paradoxus

overall_design: Examination of gene expression changes across lifespans of 76 wild yeast isolates.

first: Siming

last: Ma

first: Xuming

last: Zhou


title: Next Generation Sequencing Facilitates Quantitative Analysis of VSV-stimulated Wild Type and lncRNA-ISIR -/- spleen Transcriptomes

first: Junfang

last: Xu

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways.
Methods: spleen mRNA profiles of 8-weeks-old WT and lncRNA-ISIR, used to be called lnRNA-IRF3, knockout mice were generated by deep sequencing, using BGISEQ-500 system.
The sequence reads that passed quality filters were analyzed at the transcriptional level with RSEM (RNA-seq by Expectation Maximization).
Conclusions: Our study represents the first detailed analysis of retinal transcriptomes,  generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: spleen mRNA profiles of 8-weeks-old WT and lncRNA-ISIR-/- mice were generated by deep sequencing,  using BGISEQ-500.

first: Xuetao

last: Cao


title: Swc4 protects chromatin against genome instability and aneuploidy

first: Jia-Cheng

last: Liu

address: 320 Yue Yang Road

institute: CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences

summary: In the baker’s yeast Saccharomyces cerevisiae, Swc4, Yaf9, Arp4, and Act1 form a submodule shared by histone acetylation NuA4 complex and chromatin remodeling SWR1 complex (SWR1-C). Act1 and Arp4 are essential for cell survival. Deletion of SWC4, but not YAF9, results in severe growth defect, however, the underlying mechanism remains largely unknown. Here, we show that swc4Δ, but not yaf9Δ, eaf1Δ, or swr1Δ cells display mitotic defects in both faithful chromosome segregation and DNA ploidy, suggesting that the defects observed in swc4Δ cells are independent of the integrity of either NuA4 or SWR1-C. Additionally, loss of Swc4 function results in chromosomal breakage, spindle assembly check-point activation and significant increase of the Rfa1 foci and γ-H2A levels. Notably, both telomeres and rDNA loci in swc4Δ cells become unstable and are highly susceptible to recombination. Mechanistically, Swc4 interacts with chromatin likely through hypoacetylated histone H4. Taking together, we conclude that the chromatin associated Swc4 protects chromatin from breakage to ensure genome integrity.

overall_design: Examination of the enrichment of myc tagged Swc4  on chromatin in the budding yeast.


title: Overlapping functions of RBBP4 and RBBP7 in regulating cell proliferation and histone H3.3 deposition during mouse preimplantation development [ChIP-seq]

first: Kun

last: Zhang

address: 866 Yuhangtang Rd

summary: Preimplantation development is critical for reproductive successes in mammals. Thus, it is important to understand how preimplantation embryogenesis is regulated. As a key event of preimplantation development, epigenetic reprogramming has been widely studied, yet how epigenetic complexes regulate preimplantation development remains largely unknown. Retinoblastoma binding protein 4 (RBBP4) and 7 (RBBP7) are integral components of epigenetic complexes including SIN3A, NuRD, and CoREST. Here, we demonstrate that double knockdown of Rbbp4 and 7, but not individually, causes embryonic lethality during the morula-to-blastocyst transition. Mechanistically, depletion of RBBP4 and 7 results in dysregulation of genes related to cell cycle, lineage development, and regulation of transcription, which is accompanied by cell cycle block, disrupted lineage specification and chromatin structure. Interestingly, RBBP4/7 depletion leads to a dramatic increase in H3.3 and H3K27ac abundance during morula-to-blastocyst transition. ChIP-seq analysis in early embryos and embryonic stem cells reveals enrichment of H3.3 at the promoter regions of RBBP4/7 target genes. In summary, our studies demonstrate the compensatory role of RBBP4/7 and reveal its potential mechanisms in preimplantation development.

overall_design: Examination of H3K27ac  genomic distribution by ULI-NChIP-seq in E3.25 mouse embryos

first: Lieying

last: Xiao

first: Yanna

last: Dang


title: Overlapping functions of RBBP4 and RBBP7 in regulating cell proliferation and histone H3.3 deposition during mouse preimplantation development

overall_design: Refer to individual Series


title: Overlapping functions of RBBP4 and RBBP7 in regulating cell proliferation and histone H3.3 deposition during mouse preimplantation development [RNA-seq]

overall_design: PolyA RNA profiles of mouse and bovine embryos

first: Bingjie

last: Hu


title: Transcriptome analyses of in vitro exercise by EPS and adrenaline

status: Public on Nov 06 2021

city: Paris

first: iori

last: sakakibara

address: 22 rue Méchain

institute: Cochin institut

summary: To evaluate transcriptomic changes induced by in vitro exercise, we established two in vitro exercise models; EPS (electrical pulse stimulation and clenbuterol treatment). As for clen-buterol treatment, differentiated C2C12 myotubes were treated by 30 ng/ml clenbuterol for 1 hour and control and clenbuterol treated C2C12 myotubes were analyzed by RNA-sequencing. As for an EPS model, EPS was applied to differentiated C2C12 myotubes for 24 hours and control and EPS applied C2C12 myotubes were analyzed by RNA-sequencing.

overall_design: Examination of 2 different in vitro exercise models (EPS and clenbuterol)  in C2C12 myotubes.

first: Iori

last: Sakakibara

first: Taku

last: Fukushima


title: MCLR-elicited hepatic fibrosis and carcinogenic gene expression changes persist in rats with diet-induced nonalcoholic steatohepatitis through a 4-week recovery period

city: Spokane

first: John

middle: D.

last: Clarke

state: Washington

address: 412 E. Spokane Falls Blvd., 412 E. Spokane Fall BLVD

department: Pharmaceutical Sciences

institute: Washington State University

summary: Nonalcoholic steatohepatitis (NASH) causes liver extracellular matrix (ECM) remodeling and is a risk factor for fibrosis and hepatocellular carcinoma (HCC).   Microcystin-LR (MCLR) is a hepatotoxin produced by fresh-water cyanobacteria that causes a NASH-like phenotype, liver fibrosis, and is also a risk factor for HCC.   The focus of the current study was to investigate and compare hepatic recovery after cessation of MCLR exposure in healthy versus NASH animals.   Male Sprague-Dawley rats were fed either a control or a high fat/high cholesterol (HFHC) diet for eight weeks. Animals received either vehicle or 30 µg/kg MCLR (i.p: 2 weeks, alternate days).   Animals were euthanized at one of three time points: at the completion of the MCLR exposure period and after 2 and 4 weeks of recovery.   Histological staining suggested that after four weeks of recovery the MCLR-exposed HFHC group had less steatosis and more fibrosis compared to the vehicle-exposed HFHC group and MCLR-exposed control group. RNA-Seq analysis revealed dysregulation of ECM genes after MCLR exposure in both control and HFHC groups that persisted only in the HFHC groups during recovery.   After 4 weeks of recovery, MCLR hepatotoxicity in pre-existing NASH persistently dysregulated genes related to cellular differentiation and HCC.   These data demonstrate impaired hepatic recovery and persistent carcinogenic changes after MCLR toxicity in pre-existing NASH.

overall_design: Eight-week old male Sprague Dawley rats (n=72) were purchased from Envigo and were maintained in 12 hour light and dark cycles. Animals were divided into two groups (n=36 per diet group) and fed (ad-libitum) either a control diet or HFHC diet for 8 weeks. Following 8 week diet period, animals were administered vehicle or MCLR via intraperitoneal injections every 48 hours for 2 weeks. Animals were euthanized at three recovery time points: 24 hours (0 week recovery), 2 weeks (2 week recovery) and 4 weeks (4 week recovery) (n=6 per diet and treatment group) after the last MCLR administration.

first: J

middle: A

last: Baron

first: Tarana

last: Arman

first: Katherine

last: Lynch


title: In vitro and in vivo transcriptome analysis of CT-26 and Colon 26 tumor models

city: Cambridge

first: Min Young

last: Lee

address: 40 Landsdowne St

institute: Takeda Pharmaceutical Company Limited

summary: To determine the transcriptomic differences between CT-26 and Colon 26, we sequenced RNA from these cell lines as well as tumors isolated ex vivo from tumor bearing animals at sizes 100, 400 and 800 mm3

overall_design: We sequences RNA from in vitro culturing CT-26 and Colon 26 as well as tumors isolated from CT-26 and Colon 26 tumor bearing mice at sizes 100, 400 and 800 mm3

first: Yosuke

last: Sato

first: Yu

last: Fu

first: Hong

first: Min

middle: Y

first: Michael

middle: H

last: Shaw


title: RNA-Seq analysis, transcriptome assembly and gene expression profile analysis for vascular smooth muscle cells with upregulation of RBM10

first: Xiangyu

address: Xiasha Rd

department: General Surgery Center

institute: Sir Run-Run Shaw Hospital

summary: To understand the role of RBM10 in the apoptosis of vascular smooth muscle cells (VSMC), we quantified the whole genome transcriptomes of VSMC that were treated by Rbm10 adenovirus (n=3) or control (n=3) for 24 h using RNA-seq. In total, we obtained over 60 million clean reads from each library after trimming adaptor sequences, low quality reads and multiple mapped reads. The clean reads were mapped to 58337 genes annotated in the human reference genome.

overall_design: Human aortic smooth muscle cells were incubated with Rbm10 adenovirus and control overnight and cultured for 24 hours. Total RNA were extracted and generated by deep sequencing, in triplicate, using Hiseq X Ten sequencer.

first: Zhang

last: Xiangyu

first: Yan

last: Jin

first: Liang

last: Kai

first: Cheng

last: Huanhuan


title: The WNT-dependent gating of MYC requires non-canonical functions of a distal CTCF binding site

city: Stockholm

first: Anita

last: Göndör

address: Nobels väg 16, KI Solna Campus, Karolinska Institutet, Box 280

department: MTC

country: Sweden

institute: Karolinska Institutet

summary: Abnormal WNT signaling increases MYC expression in colon cancer cells in part via oncogenic super-enhancer (OSE)-mediated gating of MYC to the nuclear pore. This process enables MYC transcripts to escape the higher degradation rate in the nucleus compared to the cytoplasm. By targeted mutation, we show here that a single OSE-specific CTCF binding site (CTCFBS) mediates the WNT-regulated increased nuclear export rate of mRNAs derived from its interacting MYC and FAM49B loci, located >0.5 and >2.6 mbp distal of the OSE. The CTCFBS coordinated OSE-MYC proximity with their peripheral localisation, and mediated the WNT-dependent recruitment of the nuclear pore anchor AHCTF1 to the OSE. Furthermore, the CTCFBS up-regulated CCAT1 eRNA transcription, implicated in OSE-MYC interactions, correlating with an enhanced ability of the OSE to reach the nuclear periphery. We submit that WNT-dependent gating of MYC requires CTCF complexed with the OSE to coordinate multiple steps of the gating process.

overall_design: The aim of the Nodewalk sub- project is to determine the effect of CTCF binding site mutation within the OSE on the probability of interaction between MYC and the colorectal super-enhancer.


title: CTI-2 inhibits metastasis and epithelial-mesenchymal transition of breast cancer cells by modulating MAPK signaling pathway

city: Changchun

first: hui

last: li

address: qianjinstreet

institute: jilin university

summary: Although some breast cancer patients die due to tumor metastasis rather than from the primary tumor, the molecular mechanism of metastasis remains unclear. Therefore, it is necessary to inhibit breast cancer metastasis during cancer treatment. In this case, after designing and synthesizing CTI-2, we found that CTI-2 treatment significantly reduced breast cancer cell metastasis in vivo and in vitro. Notably, with the treatment of CTI-2 in breast cancer cells, the expression level of E-cadherin increased, while the expression level of N-cadherin and vimentin decreased. In addition, after CTI-2 treatment, those outflow levels for p-ERK, p-p38, and p-JNK diminished, while no significant changes in the expression levels of ERK, JNK, or p38 were observed. Our conclusion suggested that CTI-2 inhibits the epithelial-mesenchymal transition (EMT) of breast carcinoma cells by inhibiting the activation of the mitogen-activated protein kinase (MAPK) signaling pathway, thereby inhibiting the metastasis of breast tumor cells. Therefore, we believe that CTI-2 is another candidate for breast tumor medication.

overall_design: The mRNA profile of MDA-MB-231 cells treated with or without CTI-2 for 24 hours

first: Junfeng

last: Ke


title: Selective inhibition of mutant IDH1 by DS-1001b ameliorates aberrant histone modifications and impairs tumor activity in chondrosarcoma

city: Durham

first: Makoto

last: Nakagawa

state: NC

address: 308 Research Drive

department: Department of Orthopaedic Surgery

institute: Duke University

summary: Mutations in isocitrate dehydrogenase (IDH) genes occur in various malignant tumors including chondrosarcoma. IDH mutations contribute to malignant transformation by catalyzing the production of 2-hydroxyglutarate (2-HG), a competitive inhibitor of α-ketoglutarate-dependent dioxygenases. Mutant IDH inhibitors are therefore potential novel anticancer drugs in IDH mutant tumors. Here, we examined the efficacy of the inhibition of mutant IDH1 as an antitumor approach in chondrosarcoma cells in vitro and in vivo, and investigated the association between the IDH mutation and chondrosarcoma cells.

overall_design: Examination and comprison of transcriptomes of chondrosacoma cells with or without DS-1001b treatment.

first: Issay

last: Kitabayashi

first: Fumihiko

last: Nakatani


title: ChIP-seq of EgAGL9 transcription factor

status: Public on Nov 05 2021

city: Hainan

first: zhang

last: qing

address: 58 renmin avenue

department: Department of Biotechnology, College of Tropical Crops Hainan University, Haikou 570228, Hainan, China

institute: hainan university

summary: We report the result of CHIP-seq of EgAGL9 transcription factor in Elaeis guineensis Jacq.

overall_design: Eg-F1-INPUT and Eg-F1-IP.

first: Qing

last: Zhang

first: Dongdong

last: Li


title: Transcriptomic comparison among four rapeseed inbred lines with high/low linolenic acid trait

city: Yangling

first: Chengyu

last: Yu

state: Shaanxi

address: 3 Taicheng Road

department: College of Agronomy

institute: Northwest A&F University

summary: Two rapeseed germplasms named YH25005 and R8Q10 that contain 15% to 21% α-linolenic acid (ALA) in the seed fatty acids was developed and high linolenic acid trait is a new goal to improve the nutritional quality. In order to identify the important biological pathways underpinning high/low linolenic acid trait,  the transcriptome profiles of the 24-days-old embryos of YH25005 and R8Q10 was compared to that of two low linolenic acid inbred lines named A28 and SW, by using Illumina RNA-seq. We identified 6140, 8830,  9868, and 11846 differential expression genes in pairewise transcriptomic comparison of R8Q10 vs A28, YH25005 vs A28, R8Q10 vs SW, and YH5005 vs SW, respectively. It was found that some key genes related to fatty acid biosynthesis process, including LEC1, TT8, TT12, FAB1, KASII, FUS3, LEC2, FaTA, FATB, FAD7, ABI3, FAD3, KASI, SUA, Lox1 and Lox2, were significantly altered in YH25005 and R8Q10.

overall_design: Comparison among the embryos of high linolenic acid lines and that of low linolenic acid inbred lines

first: Xiaohan

first: Jinglong

last: Lian


title: Maternal circulating microRNAs altered in fetal growth restricted pregnancies

city: Manchester

first: Bernadette

middle: Carolyn

last: Baker

state: Lancashire

address: Oxford Road

department: Maternal and Fetal Health Research Centre

institute: University of Manchester

summary: Total RNA isolated from maternal serum (drawn between 36-37 weeks gestation)from pregnancies with a growth restricted infant defined as an Individualised birthweight centile (IBC) < 3rd matched to a  control pregnancy (IBC 20-80th), n=4 per group with 2 female and 2 male infants per group. Maternal serum miRNAs profiled using miRCURY LNA Universal RT miRNA PCR Human panel I + II to determine biomarker potential for prediction of growth restriction and sexually dimorphic patterns.

overall_design: RT-qPCR microRNA expression profiling of total RNA isolated from maternal serum from women at 36weeks of pregnancy with growth restricted infant defined as an Individualised birthweight centile (IBC) < 3rd matched to a  control pregnancy (IBC 20-80th), n=4 per group with 2 female and 2 male infants per group.

first: Karen

last: Forbes